Field of the Invention
The present invention is in the field of methods and genotyping panels for detecting alleles, genomes, and transcriptomes in admixtures of two individuals.
Description of the Related Art
Prenatal diagnostic methods are primarily aimed at obtaining genetic information of a fetus or an embryo. Prenatal genetic diagnostic methods used in clinical practice essentially involve invasive techniques such as amniocentesis, the removal of chorionic villi, and the removal of fetal blood or tissue biopsies. Those techniques involve obtaining samples directly from the fetus or indirectly from female reproductive structures. Because of the highly invasive nature of those methods, they are prone to complications for the mother or the fetus. Examples of such complications which can be cited in the case of amniocentesis are the risk of infection, feto-maternal hemorrhage with possible allo-immunization, loss of amniotic fluid and abdominal pain. Different studies have estimated the risk of a miscarriage after amniocentesis at 0.06% to 2.1% higher than that of the control group (Eddleman, Obstet Gynecol 2006 108(5): 1067-1072). As a result, amniocentesis is only suggested for women for whom the risk of having a child with a clinically significant genetic variation exceeds that of iatrogenic miscarriage, and many physicians prefer to cite a risk commensurate with their experience (typically 1 in 300 to 1 in 500).
In order to limit the use of invasive prenatal diagnostic techniques risking the complications mentioned above and which are generally disagreeable and/or the source of stress for the mother, the development of non-invasive methods constitutes a major aim in modern obstetrics.
In particular, fetal cells circulating in maternal blood constitute a source of genetic material that is of potential use for prenatal genetic diagnosis (Bianchi, Br J Haematol 1999 105: 574-583; Fisk, Curr Opin Obstet Gynecol 1998 10: 81-83). During pregnancy, different cell types of fetal origin traverse the placenta and circulate in the maternal blood (Bianchi, Br J Haematol 1999 105: 574-583). Such cell types include lymphoid and erythroid cells, myeloid precursors and trophoblastic epithelial cells (cytotrophoblasts and syncytiotrophoblasts).
Methods for analyzing the genome of fetal cells circulating in maternal blood with a view to prenatal diagnosis have been described, but they remain relatively limited regarding sensitivity and the specificity of the diagnosis (Di Naro et al., Mol Hum Reprod 2000 6: 571-574; Watanabe et al., Hum Genet 1998 102: 611-615; Takabayashi et al., Prenat Diagn 1995 15: 74-77; Sekizawa et al., Hum Genet 1998 102: 393-396). The advantage in developing a non-invasive, highly specific prenatal diagnosis method results from the possibility of using it to reduce the proportion of invasive diagnostic methods carried out in pregnant women for whom the result is negative in the end. By way of example, in the case of trisomy 21, which concerns one woman in 700, prenatal diagnosis is currently offered in France only if the mother is 38 years old, while a biochemical analytical test capable of detecting 60% of trisomy 21 cases for 5% of the price of amniocentesis is proposed for younger women. However, 40% of trisomy 21 cases are not detected by currently available tests. Prenatal detection of trisomy 21 in fetal cells isolated from the maternal plasma using a FISH technique has been described. That approach is interesting, but as fetal cells are rare in plasma (1 in 500 to 1 in 2000) and often include apoptotic cells, reliable diagnosis would require carrying out the method on a very large number of cells, rendering it impossible to carry out routinely. Further, euploid fetal cells cannot be identified by that approach.
One limitation of such approaches derives from the fact that fetal cells circulating in the blood are present in very low concentrations. Studies based on PCR detection of the Y chromosome in blood samples without prior selection have allowed the mean number of fetal cells to be determined to be about one fetal lymphocyte cell per milliliter of blood (Bianchi, J Perinat Med 1998 26: 175-85). More recently, the mean number of fetal cells has been revised upward as improved enrichment techniques yield more cells. One recent study found a mean value of 37 fetal lymphocytes per milliliter of blood. (Huang, Prenatal Diagnosis 2008 28: 892-899).
Thus, there is a need for improved methods and tools for detecting fetal alleles and fetal genetic variations.